I am in the midst of writing my second NaNo novel, and I have encountered a problem I didn't anticipate. It is similar to this question, about changing a character's name in the middle of a story, but the situation in my story is different enough that I think it will need a different answer.

In the first part of the story, we meet the protagonist, Nicene. After a second part (which isn't written yet), she is discovered unconscious on the streets by Shadow. During this period, the story is from Shadow's point of view and she is 'the woman'. After she regains consciousness, she tells him that her name is Cherry, and so the narrative continues with her named as Cherry. The trouble is, I am sliding back into her point of view, but I haven't let the reader know that this woman is actually Nicene.

I don't really want it to be a surprise to the reader when they find out who she is, so I have made several connections between the prior part and the current part, and Shadow has made it obvious that he doesn't believe that Cherry is her real name. I am on the verge of revealing her honorifics, which are important and should be a surprise, but might also further confuse the reader.

I am stuck on how to transition from the viewpoint of someone who doesn't know her real name ('Cherry') back to her ('Nicene'), because Nicene certainly doesn't think of herself as Cherry—that's just an alter ego—but the reader might not have realized who she really is.

Your answer is the closest to what I ended up doing, which is that earlier in the story she lifts a fake ID off someone, and laughs about the name to her friend -- "Hey, this one says her name is Cherry..." so that the name is familiar to the reader later, and the reader can guess that it is Nicene. I felt the other methods (distinctive feature, catchphrase, etc) were too intrusive in the writing style for this story.
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Kit Z. FoxDec 9 '13 at 21:40

My suggestion would be almost the polar opposite of Stephan's; I think you ought to try switching back to Nicene/Cherry's viewpoint, at least temporarily, very soon after she's found by Shadow. While in her viewpoint, make sure to have Shadow address her as "Cherry", while consistently using her real name in narrative and any internal thoughts. Done right, this should make it clear to the reader that these two names refer to the same person.

In particular, one option would be to retell the initial encounter from both characters' viewpoints. That way, you can first describe from Shadow's viewpoint how he finds the strange unconscious woman, and have her introduce herself as Cherry, and then (immediately, or at least fairly soon) switch back to her viewpoint and show how she feels about waking up and being confronted by a strange man, and then directly show what she's thinking as she decides to give a false name for herself. You can then continue the story for a while from her viewpoint, and then, if you want, switch back to his when a convenient opportunity presents itself.

Of course, giving some clues (like, say, a distinctive physical appearance, as suggested in some of the other answers) about Nicene/Cherry's identity even before you switch to her viewpoint could help further reduce the interval during which the reader might be unsure of who she it. Still, even if you deliberately go out of your way not to provide any such clues, it could still work as long as you do the viewpoint switch soon enough. In fact, one possible opportunity for the switch might be immediately after she introduces herself as Cherry:

"You can call me Shadow," he said. "It's as good a name as any. And what's your name, sweetheart?"

The woman took a while to reply, her eyes flicking between his face and the room, as if she was trying to make a decision. "Cherry. My name's Cherry," she said.

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The first thing Nicene became aware of was the pain in her head. The pain, and the strange fleeting lights and shapes that slowly gave way to an unfamiliar room as she opened her eyes. In the doorway, watching her, stood a man she didn't recognize. She wasn't sure how long he'd been there, but he seemed content to just stand there and wait as she gathered her senses.

"Who are you?" she asked the man. It didn't seem like the most original thing to ask, but then, she wasn't feeling very original right then. "What is this place?" she continued.

"You can call me Shadow," he said. "It's as good a name as any. And what's your name, sweetheart?"

(Apologies for stealing your character names for the example above. Any resemblance of the example, or of the characters in it, to your actual story should be considered entirely coincidental.)

My first instinct would be to abstain from writing from Cherry's perspective until her identity is revealed, thereby making her more of a mystery character. Since Nicene is the protagonist, however, that probably won't work, unless you have a second protagonist to focus on during that time.

I recommend using the name Cherry when writing from her perspective, but as Dale Emery suggests in his answer, use her thoughts to reveal to the reader that this is not her real name. You could write things like, "Cherry, as Shadow calls her, ..." or "The woman known to Shadow as Cherry ..."

Incidentally, there is a very good example of such a character in Abaddon's Gate by James SA Corey. One of the characters refers to herself by her fake name, and makes it clear that this name is indeed fake, without revealing her true identity. I think this technique can work regardless of the character's own level of investment in the name.

There are many stories where characters take on false names. In the dialogue, this person goes by the fake name. In the narrative (the part of the text not directly quoted from the speech of the characters) the person goes by the true name. No confusion for the reader about who this person is, because the true name always stays the same.

I think this would be more confusing, since it is written from Shadow's point of view, and he only knows her as Cherry.
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Kit Z. FoxNov 14 '13 at 11:52

You wrote that you don't need the reader to be misled. So I assume an omniscient narrator, which is possible even if you tell the story from the perspective of one character: "When Shadow met Nicene, he only knew her as Cherry, because that was the name she had given him." or something to that effect. That way you have an omniscient narrator telling the reader what the protagonist doesn't know.
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whatNov 14 '13 at 11:58

Give Nicene some clear, identifying characteristic. She has purple hair; she doesn't let anybody touch her; she refers to any sort of weapon as a "thingamabob"; whatever. Then, whenever it is you want the reader to understand who she is, you just let her "tell" show:

"I'm Cherry," the woman said. She wasn't looking him in the eyes; instead, she was examining his sword cautiously. "Say," she said, "nice thingamabob you've got there."

It's particularly effective if you also provide some standard clue that she's not using her real name. What you're doing here is relying on narrative convention - sure, Cherry could be some complete stranger who happens to have the same mannerism, but the reader understands that this is your way of identifying her for who she really is.

Whatever hinting you can give as to Cherry being a false identity will be helpful - the moment the reader recognizes your character, they'll be wondering why she's in hiding, so you should either answer that question, or else simply acknowledge it every now and again, until it's time to give the answer. That way the reader knows that you, the author, haven't simply forgotten about a huge plot hole, and the they, the reader, haven't missed the crucial dozen pages explaining everything that's going on.